rs2246477

Variant names:

• chr5-172781451-A-G
• rs2246477
• ENST00000650258.1:n.506-621A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-172781451-A-G
• chr5-172781451-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_188285.1(LOC105377730):​n.697-621A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,246 control chromosomes in the GnomAD database, including 1,554 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.12 (1554 hom., cov: 32)
• Consequence: LOC105377730 NR_188285.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228
• Publications: 6 publications found

Genes affected

ENSG00000253736 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_188285.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105377730	NR_188285.1		n.697-621A>G		intron	N/A
	LOC105377730	NR_188287.1		n.479-621A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253736	ENST00000650258.1		n.506-621A>G		intron	N/A
	ENSG00000289170	ENST00000692849.2		n.89+6846T>C		intron	N/A
	ENSG00000289170	ENST00000792515.1		n.148+6657T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18710 AN: 152128 Hom.: 1551 Cov.: 32

Gnomad AFR AF: 0.0344

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.00384

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.141

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.123 AC: 18723 AN: 152246 Hom.: 1554 Cov.: 32 AF XY: 0.121 AC XY: 9015 AN XY: 74446

African (AFR) AF: 0.0346 AC: 1439 AN: 41566

American (AMR) AF: 0.114 AC: 1737 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 578 AN: 3470

East Asian (EAS) AF: 0.00385 AC: 20 AN: 5194

South Asian (SAS) AF: 0.168 AC: 808 AN: 4822

European-Finnish (FIN) AF: 0.135 AC: 1431 AN: 10592

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12206 AN: 67992

Other (OTH) AF: 0.138 AC: 291 AN: 2104

Alfa AF: 0.138 Hom.: 253

Bravo AF: 0.117

Asia WGS AF: 0.0790 AC: 275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.2
DANN	Benign	0.84
PhyloP100		0.23

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2246477; hg19: chr5-172208454;